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LOC108281185 nontranscribed DNase I hypersensitive site-defined enhancer upstream of RPS3AP9 [ Homo sapiens (human) ]

Gene ID: 108281185, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281185
Gene description
nontranscribed DNase I hypersensitive site-defined enhancer upstream of RPS3AP9
Gene type
biological region
Feature type(s)
regulatory: DNase_I_hypersensitive_site, enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located approximately 26 kb upstream of the RPS3AP9 (ribosomal protein S3a pseudogene 9) locus. It was defined as a nontranscribed region with regulatory potential based on the presence of a DNase I hypersensitive site (DHS), with an absence of capped transcripts by cap analysis of gene expression (CAGE) in HeLa cells. It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
1q31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (188668052..188668618)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (188014194..188014760)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (188637183..188637749)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 156 Neighboring gene DEAD-box helicase 19B pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:188324587-188325088 Neighboring gene HERV-FRD provirus ancestral Env polyprotein pseudogene Neighboring gene RPS3A pseudogene 9

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • no CAGE DHS FANTOM5 enhancer upstream of RPS3AP9

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051145.1 

    Range
    101..667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    188668052..188668618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    188014194..188014760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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